The issue is that the initial indentation of children below the last expanded parent is incorrect (too small).

Below is a code example which:

- creates and shows an empty treeView
- for visual clarity: has a style rule for the disclosure node with large left padding and yellow background
- builds a treeItem hierarchy of nested items that is attached to the tree _after_ showing
- expected: every child has a larger indentation than its parent
- actual: some have a smaller indentation
- click on any item to select it and see the broken layout to jump to the expected location

notes:
- layout is as expected if the data is added before showing
- the jumping can be seen also without custom style, but is slight in that case
- the mis-location seems to start at the first child of the last expanded parent (and all items below that)
- the issue was brought up at SO https://stackoverflow.com/q/72625590/203657
- digging done in that question reveals a diffferent state of the isNeedsLayout flag of cells when comparing fx8/fx18

The broken layout is a regression: working as expected in fx8, fx11, broken in fx17. Might be technically introduced with JDK-8252811 (fixed after fx15) - reverting that change of VirtualFlow made the layout look okay. On the other hand, this might be a bit accidental (the layout flag looks inconsistent since fx11), feels like there's a cell layout update path that's not fully covered. Also (as noted in the question/answer on SO) the indenting code in TreeCellSkin looks fishy.

The example:

public class TreeViewLayoutBug extends Application {

    @Override
    public void start(Stage primaryStage) throws Exception {
        final TreeView<String> tree = new TreeView<>();
        BorderPane root = new BorderPane(tree);
        final Scene scene = new Scene(root, 250, 300);
        scene.getStylesheets().add(this.getClass().getResource("treeviewlayoutissue.css").toExternalForm());
        String version = System.getProperty("javafx.runtime.version");
        primaryStage.setTitle("TreeView " + version);
        primaryStage.setScene(scene);
        primaryStage.show();

        // set data after showing the tree
        addData(tree);

    }

    private void addData(TreeView<String> tree) {
        // build the item hierarchy
        final TreeItem<String> rootNode = new TreeItem<>("root");
        rootNode.setExpanded(true);
        final TreeItem<String> firstChild = new TreeItem<>("Child A");
        final TreeItem<String> secondChild = new TreeItem<>("Child B");
        rootNode.getChildren().addAll(firstChild, secondChild);

        final TreeItem<String> grandChild = new TreeItem<>("GrandChild A");
        firstChild.getChildren().addAll(grandChild);
        // variants of added grand/grand children to see intial broken layout
        // moving to first child of last expanded parent
// secondChild.getChildren().add(new TreeItem<>("GrandChild B"));
//
// final List<TreeItem<String>> groups = Stream.of("Red", "Green", "Yellow", "Blue").map(TreeItem::new).collect(Collectors.toList());
// groups.forEach(itm -> grandChild.getChildren().add(itm));

        firstChild.setExpanded(true);
        secondChild.setExpanded(true);
        grandChild.setExpanded(true);
        // set root - note: doing at the end to not have effect of showRoot
        tree.setRoot(rootNode);
    }

    public static void main(String[] args) {
        launch(args);
    }

}

The style:

.tree-cell > .tree-disclosure-node{
    -fx-padding: 4 6 4 50;
    -fx-background-color: yellow;
}